BCFTools liftover SWAP - investigate and re-enable?
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enhancement
- Dominant language
- Python
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Description
See issue SACGF/variantgrid_private#3763
BCFTools liftover flags a variant that changes to a reference base via SWAP info flag. Because we deal in variants not genotypes, we are not sure our implementation is correct, so we disabled this via
`settings.BCFTOOLS_LIFTOVER_ALLOW_SWAP=False`
So these currently fail liftover. It might be worth investigating this and trying to get it to work? It is pretty rare.
During the work I noticed I was only handling `SWAP=1` so maybe look there?
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